After her werewolf lover unexpectedly dies in an accident, a woman must find a way to raise the son and daughter that she had with him. However, their inheritance of their father's traits prove to be a challenge for her.

主角绯村剑心流浪至东京，因为神谷薰的挽留而留在东京。其后认识了明神弥彦、相乐左之助及高荷惠等人，又与前幕府杀手鹈堂刃卫、御庭番众首领四乃森苍紫决斗，其间剑心经历了多次战斗，令剑心自觉慢慢变回昔日的刽子手拔刀斋（千人斩拔刀斋）（人斩り抜刀斎）。最后在与幕末时代的对手前新撰组第三小队组长斋藤一决战及得知志志雄一党的阴谋后，独自前往京都与志志雄一党对决。